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- PDB-1lqj: ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE -

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Basic information

Entry
Database: PDB / ID: 1lqj
TitleESCHERICHIA COLI URACIL-DNA GLYCOSYLASE
ComponentsURACIL-DNA GLYCOSYLASE
KeywordsHYDROLASE / GLYCOSYLASE / DNA REPAIR / BASE EXCISION
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / cytoplasm
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...Uracil-DNA glycosylase family 1 / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsSaikrishnan, K. / Sagar, M.B. / Ravishankar, R. / Roy, S. / Purnapatre, K. / Varshney, U. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG.
Authors: Saikrishnan, K. / Bidya Sagar, M. / Ravishankar, R. / Roy, S. / Purnapatre, K. / Handa, P. / Varshney, U. / Vijayan, M.
#1: Journal: Nucleic Acids Res. / Year: 1998
Title: X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (ECUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG
Authors: Ravishankar, R. / Sagar, M.B. / Roy, S. / Purnapatre, K. / Handa, P. / Varshney, U. / Vijayan, M.
#2: Journal: Protein Expr.Purif. / Year: 1998
Title: Use of a coupled transcriptional system for consistent overexpression and purification of UDG-UGI complex and ugi from Escherichia coli
Authors: Roy, S. / Purnapatre, K. / Handa, P. / Boyanapalli, M. / Varshney, U.
#3: Journal: J.Mol.Biol. / Year: 1999
Title: Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase.
Authors: Putnam, C.D. / Shroyer, M.J.N. / Lundquist, A.J. / Mol, C.D. / Arvai, A.S. / Mosbaugh, D.W. / Tainer, J.A.
History
DepositionMay 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: URACIL-DNA GLYCOSYLASE
B: URACIL-DNA GLYCOSYLASE
C: URACIL-DNA GLYCOSYLASE
D: URACIL-DNA GLYCOSYLASE


Theoretical massNumber of molelcules
Total (without water)102,9014
Polymers102,9014
Non-polymers00
Water3,153175
1
A: URACIL-DNA GLYCOSYLASE


Theoretical massNumber of molelcules
Total (without water)25,7251
Polymers25,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: URACIL-DNA GLYCOSYLASE


Theoretical massNumber of molelcules
Total (without water)25,7251
Polymers25,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: URACIL-DNA GLYCOSYLASE


Theoretical massNumber of molelcules
Total (without water)25,7251
Polymers25,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: URACIL-DNA GLYCOSYLASE


Theoretical massNumber of molelcules
Total (without water)25,7251
Polymers25,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.210, 125.210, 90.047
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Cell settingtrigonal
Space group name H-MP32

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Components

#1: Protein
URACIL-DNA GLYCOSYLASE / / E.C.3.2.2.- / UDG / URACIL-DNA-GLYCOSYLASE


Mass: 25725.182 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P12295, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20mM Tris-HCl, 100mM NaCl, 15% PEG 8000, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 293K, temperature 293.0K
Crystal grow
*PLUS
Temperature: 293 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
220 mMTris-HCl1droppH7.4
3100 mM1dropNaCl
415 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.35→20 Å / Num. all: 20394 / Num. obs: 20394 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Rsym value: 0.154 / Net I/σ(I): 6.9
Reflection shellResolution: 3.35→3.47 Å / Mean I/σ(I) obs: 1.4 / Rsym value: 0.369 / % possible all: 94.8
Reflection
*PLUS
Num. measured all: 38941 / Rmerge(I) obs: 0.154
Reflection shell
*PLUS
% possible obs: 94.8 % / Rmerge(I) obs: 0.369

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UUG

1uug


Resolution: 3.35→20 Å / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.326 1101 5.8 %RANDOM
Rwork0.241 ---
obs0.241 18979 84 %-
all-18979 --
Displacement parametersBiso mean: 28.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.4 Å
Luzzati d res low-10 Å
Luzzati sigma a0.51 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 3.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7157 0 0 175 7332
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_improper_angle_d0.91
LS refinement shellResolution: 3.35→3.56 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.353 171 -
Rwork0.271 --
obs-2887 81.1 %
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.91

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